[ensembl-dev] VEP feature requests

Michael Yourshaw myourshaw at ucla.edu
Tue Jan 17 01:20:48 GMT 2012


Here are a few suggestions that would be useful for VEP plugin developers.

1. Make the original input line available to plugins. I do this by patching VEP.pm, sub init_line, after "my $line = …", to add:

    $line->{_input_line} = $vf->{_line};

2. Provide a way to preserve columns with a value of zero instead of converting to ‘-‘. I do this in variant_effect_predictor.pl , sub print_line,  by changing:

       #$output = join "\t", map { $line->{$_} || '-' } @OUTPUT_COLS;
        $output = join "\t", map { $line->{$_} } @OUTPUT_COLS;

3. Provide a way for plugins to see intergenic variants (when there is no regulatory or transcript variation). It looks like the solution to this one is a bit more complex, and may interact with my earlier post about problems with not fully qualified feature types.

ॐ

Michael Yourshaw
UCLA Geffen School of Medicine
Department of Human Genetics, Nelson Lab
695 Charles E Young Drive S
Gonda 5554
Los Angeles CA 90095-8348 USA
myourshaw at ucla.edu
970.691.8299

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